An alcohol dehydrogenase ribozyme

Nature Structural Biology

Volumn 10, Issue 9, 2003, Pages 713-717

  Tsukiji, Shinya ^a   Pattnaik, Swetansu B ^a   Suga, Hiroaki ^a  

^a UNIVERSITY AT BUFFALO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE PHOSPHATE; ADENOSINE TRIPHOSPHATE; ALCOHOL DEHYDROGENASE; DNA; FLAVINE ADENINE NUCLEOTIDE; NICOTINAMIDE ADENINE DINUCLEOTIDE; REDUCED NICOTINAMIDE ADENINE DINUCLEOTIDE; RIBOZYME; RNA;

ARTICLE; CATALYSIS; ENZYME ACTIVITY; ENZYME KINETICS; EVOLUTION; MICHAELIS MENTEN KINETICS; NONHUMAN; NUCLEOTIDE SEQUENCE; OXIDATION REDUCTION REACTION; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL;

ALCOHOL DEHYDROGENASE; BASE SEQUENCE; EVOLUTION, MOLECULAR; FLAVIN-ADENINE DINUCLEOTIDE; MODELS, CHEMICAL; MOLECULAR SEQUENCE DATA; NAD; OLIGONUCLEOTIDES; OXIDATION-REDUCTION; OXYGEN; RNA; RNA, CATALYTIC;

EID: 0042320360     PISSN: 10728368     EISSN: None     Source Type: Journal    
DOI: 10.1038/nsb964     Document Type: Article

References (30)

1. Berg, J.M., Tymoczko, J.L. & Stryer, L. Biochemistry (Freeman, New York, 2002).
2. Gray, H.B. & Ellis, J.W.R. Electron transfer. In Bioinorganic Chemistry (eds. Bertini, I., Gray, H.B., Lippard, S.J. & Valentine, J.S.) 315-363 (University Science Books, Sausalito, California, USA, 1994).
3. Gilbert, W. The RNA world. Nature 319, 618 (1986).
4. White, H.B., III. Coenzymes as fossils of an earlier metabolic state. J. Mol. Evol. 7, 101-104 (1976).
5. Joyce, G.F. & Orgel, L.E. Prospects for understanding the origin of the RNA world. In The RNA World (eds. Gesteland, R.F., Cech, T.R. & Atkins, J.F.) 49-77 (Cold Spring Harbor Laboratory Press, New York, 1999).
6. Benner, S.A., Ellington, A.D. & Tauer, A. Modern metabolism as a palimpsest of the RNA world Proc. Natl. Acad. Sci. USA 86, 7054-7058 (1989).
7. Bertini, I. & Luchinat, C. The reaction pathways of zinc enzymes and related biological catalysts. In Bioinorganic Chemistry (eds. Bertini, I., Gray, H.B., Lippard, S.J. & Valentine, J.S.) 37-106 (University Science Books, Sausalito, California, USA, 1994).
8. Konarska, M.M., Grabowski, P.J., Padgett, R.A. & Sharp, P.A. Characterization of the branch site in lariat RNAs produced by splicing of mRNA precursors. Nature 313, 552-557 (1985).
9. Burgin, A.B. & Pace, N.R. Mapping the active site of ribonuclease P RNA using a substrate containing a photoaffinity agent. EMBO J. 9, 4111-4118 (1990).
10. Nakamura, M., Toda, M., Saito, H. & Ohkura, Y. Fluorimetric determination of aromatic aldehydes with DDB. Anal. Chim. Acta. 134, 39-45 (1982).
11. Blankenhorn, G. Intermolecular complexes between N-methyl-1,4-dihydronicotinamide and flavines. The influence of steric and electronic factors on complex formation and the rate of flavine-dependent dihydronicotinamide dehydrogenation. Biochemistry 14, 3172-3176 (1975).
12. Kimura, E., Shionoya, M., Hoshino, A., Ikeda, T. & Yamada, Y. A model for catalytically active zinc(II) ion in liver alcohol dehydrogenase: a novel "hydride transfer" reaction catalyzed by zinc(Il)-macrocyclic polyamine complexes. J. Am. Chem. Soc. 114, 10134-10137 (1992).
13. + model compound. Bull. Chem. Soc. Jpn. 57, 1435-1436 (1984).
14. Mathews, D.H., Sabina, J., Zuker, M. & Turner, D.H. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol. 288, 911-940 (1999).
15. Sassanfar, M & Szostak, J.W. An RNA motif that binds ATP. Nature 364, 550-553 (1993).
16. Jiang, F., Kumar, R.A., Jones, R.A. & Patel, D.J. Structural basis of RNA folding and recognition in an AMP-RNA aptamer complex. Nature 382, 183-186 (1996).
17. Feigon, J., Dieckmann, T. & Smith, F.W. Aptamer structures from A to zeta. Chem. Biol. 3, 611-617 (1996).
18. Shinkai, S., Yamada, S & Kunitake, T. Coenzyme models. 10. Rapid oxidation of NADH by a flavin immobilized in cationic polyelectrolytes. Macromolecules 11, 65-68 (1978).
19. Hamachi, I. & Kobuke, Y. Facilitated electron transfer from NADH to flavolipid bound in ammonium bilayer. J. Chem. Soc., Chem. Commun., 130-131 (1989).
20. Kokubo, T., Sassa, S. & Kaiser, E.T. Flavohemoglobin: a semisynthetic hydroxylase acting in the absence of reductase. J. Am. Chem. Soc. 109, 606-607 (1987).
21. Ferre-D'Amare, A.R., Zhou, K. & Doudna, J.A. Crystal structure of a hepatitis delta virus ribozyme. Nature 395, 567-574 (1998).
22. Hilbers, C.W., Michiels, P.J. & Heus, H.A. New developments in structure determination of pseudoknots. Biopolymers 48, 137-153 (1998).
23. Yarus, M. Boundaries for an RNA world. Curr. Opin. Chem. Biol. 3, 260-267 (1999).
24. Bartel, D.P. & Unrau, P.J. Constructing an RNA world. Trends Cell Biol. 9, M9-M13 (1999).
25. Huang, F., Bugg, C.W. & Yarus, M. RNA-catalyzed CoA, NAD, and FAD synthesis from phosphopantetheine, NMN, and FMN. Biochemistry 39, 15548-15555 (2000).
26. Breaker, R.R. & Joyce, G.F. Self-incorporation of coenzymes by ribozymes. J. Mol. Evol. 40, 551-558 (1995).
27. Burgstaller, P. & Famulok, M. Isolation of RNA aptamers for biological cofactors by in vitro selection. Angew. Chem. Int. Ed. Engl. 33, 1084-1087 (1994).
28. Lauhon, C.T. & Szostak, J.W. RNA aptamers that bind flavin and nicotinamide redox cofactors. J. Am. Chem. Soc. 117, 1246-1257 (1995).
29. Roychowdhury-Saha, M., Lato, S.M., Shank, E.D. & Burke, D.H. Flavin recognition by an RNA aptamer targeted toward FAD. Biochemistry 41, 2492-2499 (2002).
30. Cadwell, R.C. & Joyce, G.F. Mutagenic PCR. PCR Methods Appl. 3. S136-S140 (1994).